The present invention relates to novel alkaliphilic and thermophilic microorganisms and to novel enzymes obtained therefrom.
Alkaliphiles are a heterogeneous group of microorganisms spread over many taxonomic groups which exhibit optimum growth in an alkaline pH environment (Jones, B. E. et al, (1994) Alkaliphiles: diversity and identification, in xe2x80x9cMicrobial Diversity and Identificationxe2x80x9d (F. G. Priest et al, Eds.) Plenum Press, New York and London, pages 195-230), generally in excess of pH 8. Obligate alkaliphiles generally have a pH optimum for growth between pH 9 and pH 10, and are incapable of growth at neutral pH. Alkalitolerant (or facultatively alkaliphilic) microorganisms are less exacting and although they are capable of growth at alkaline pH values, their optima lie in the neutral to acid pH range.
Thermophiles are also a very heterogeneous collection of microorganisms defined as having an optimum growth temperature in excess of 50xc2x0 C. For moderate thermophiles the maximum growth temperature usually lies below 70xc2x0 C. An organism with a growth minimum above 40xc2x0 C., an optimum above 65xc2x0 C., and a growth maximum above 70xc2x0 C. is defined as an extreme thermophile (Cowan, D. A. (1992) Biochemistry and molecular biology of extremely thermophilic archeaobacteria, in xe2x80x9cMolecular Biology and Biotechnology of Extremophilesxe2x80x9d (R. A. Herbert and R. J. Sharp, Eds.), Blackie and sons Ltd., Glasgow and London, pages 1-43).
The combined phenotype, alkaliphily and thermophily appears to have only rare occurrence. Only two such microorganisms, both isolated from sewage digestion plants, have been well described and both were assigned to the genus Clostridium of the Gram-positive bacteria. One of the organisms, Clostridium paradoxum, is obligately alkaliphilic growing between pH 7.3 and pH 11.0, with an optimum around pH 10. It can however, only be classified as a moderate thermophile since it has an optimum growth temperature of 55xc2x0 C. and a maximum at 63xc2x0 C. (Youhong Li et al (1992) Int. J. Syst. Bacteriol. 43, 450-460). A second organism, Clostridium thermoalcaliphilum is a facultative alkaliphile or alkalitolerant organism growing between pH 7 and pH 11, with an optimum between pH 9.5 and pH 10. With an optimum growth temperature of 50xc2x0 C. and maximum at 57xc2x0 C. this bacterium can only be classified as a very moderate thermophile or as thermotolerant (Youhong Li et al (1994) Int. J. Syst. Bacteriol. 44, 111-118).
Among the known types of thermophilic bacteria several species belong to the order Thermotogales. This distinct group of mainly extreme thermophilic bacteria has been shown by sequencing of the ribosomal RNA genes to be phylogenetically distant from all other bacteria, and to represent one of the deepest branches and most slowly evolving lineages within the Domain Bacteria. Bacteria of the Thermotogales are characteristically, Gram-negative, rod-shaped, anaerobic, fermentative bacteria with an outer sheath-like envelope (xe2x80x9ctogaxe2x80x9d); their growth is inhibited by molecular hydrogen (Huber, R. and Stetter, K. O. (1992) The order Thermotogales, in xe2x80x9cThe Prokaryotesxe2x80x9d (A. Balows et al, Eds.), Springer-Verlag, New York, pages 3809-3815).
At present, the Thermotogales are represented by five genera. The genera Thermotoga, Thermosipho and Fervidobacterium comprise the known extreme thermophilic species, while the more distantly related (on the basis of 16S rRNA analysis) genera Geotoga and Petrotoga represent the more mesophilic species. None of the known species is noticeably alkaliphilic in nature. Most of the extant species of extreme thermophilic Thermotogales have been isolated from active geothermal aquatic environments such as shallow and deep-sea marine hydrothermal systems or from low-salinity continental solfatara springs. More recently less thermophilic strains, particularly those of the genera Geotoga and Petrotoga have been isolated from deep sub-surface oil fields (Huber, R. and Stetter, K. O. (1992) ibid; Davey, M. E. et al, (1993) Syst. Appl. Microbiol. 16, 191-200; Ravot, G. et al, (1995) Int. J. Syst. Bacteriol. 45, 308-314).
Although the different members of the Thermotogales may be partially differentiated on the basis of phenotypic characteristics such as temperature, pH and NaCl ranges permitting growth (Table 1, Ravot, G. et al (1995) Int. J. Syst. Bacteriol. 45, 308-314), their classification is largely based on a comparison of similarity between nucleotide sequences on the 16S rRNA genes and DNA-DNA hybridisation studies. Stackebrandt and Goebel (Int. J. Syst. Bacteriol. 44, 846-849, 1994) suggest that strains of microorganisms having more than 97% 16S rRNA sequence identity may be considered members of the same species, provided that other criteria are also met. It has been shown that the 16S rRNA sequences of Fervidobacterium islandicum and Fervidobacterium nodosum are 95.3% similar which is typical of different species within the same genus (Huber, R. et al, (1990) Arch. Microbiol. 154, 105-111), but that these differ by 10-15% with strains of Thermotoga and Thermosipho. Within the Thermotogales sequence differences of up to about 8% have generally qualified for placing the strains in the same genus. 16S rRNA sequence differences of greater than about 10%, together with differences in phenotype have frequently been used as compelling arguments for placing different isolates of Thermotogales in separate genera (Huber, R. et al, (1989) Syst. Appl. Microbiol. 12, 32-37; Davey, M. E. et al, (1993) Syst. Appl. Microbiol. 16, 191-200; Ravot, G. et al, (1995) Int. J. Syst. Bacteriol. 45, 308-314).
The present invention provides novel thermophilic alkaliphilic bacteria of the novel genus Thermopallium, more specifically of the novel species Thermopallium natronophilum, and novel polypeptides obtainable from these bacteria. In a more specific aspect, the invention provides novel alkaline pullulanase and amylase preparations from these novel bacteria.
In a third aspect, the invention provides a composition comprising a novel polypeptide according to the invention.
In a fourth aspect, the invention provides an isolated DNA fragment encoding a polypeptide according to the invention, recombinant DNA comprising such DNA fragment, host cells transformed with such recombinant DNA and a culture of such host cells.
In another aspect, the invention provides a method for producing a polypeptide, preferably an enzyme, according to the invention.
The Microorganisms
The novel microorganisms of the present invention were isolated from hot springs and their run-off streams having an alkaline pH due to dissolved carbonate (and related anions) but having a low concentration of dissolved salts as measured by electrical conductivity (Table 2). The hot springs were located in the volcanically active regions of the Rift Valley in continental East Africa. They have typical carbonate anion concentrations in excess of 1 g/l and are therefore not typical of the usual solfatara type. A pure culture of the isolated microorganism designated Thermopallium natronophilum Tg9A has been deposited on Sep. 21, 1994 according to the Budapest Treaty on the International Recognition of the Deposits of Microorganisms for the Purpose of Patent Procedures at the DSM-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany under Accession Number DSM 9460.
The microorganism of this invention is a strictly anaerobic, rod-shaped bacterium which does not form endospores. The bacterial cell is surrounded by a characteristic sheath-like outer structure or xe2x80x9ctogaxe2x80x9d ballooning over both poles of the cell. The cells usually occur singly or in short chains of up to 3 cells long. During the growth phase the cells can become curved or irregular in shape, and sometimes form aggregates. During the stationary growth phase the cells become coccoid, with one or more cells inside a large spherical body. The microorganism forms round, shiny, whitish, translucent colonies on alkaline nutrient agar or Gelrite, containing carbonate. On the basis of these characteristics the strains of the microorganism Thermopallium natronophilum can therefore be assigned to the bacterial order xe2x80x9cThermotogalesxe2x80x9d (Huber, R. and Stetter, K. O. (1992) The order xe2x80x9cThermotogalesxe2x80x9d in: The Prokaryotes, (A. Barlows et al., eds.), Springer-Verlag, New York, pp. 3809-3815).
The natural isolates of the microorganism of the present invention can be further described by the following characteristics.
Growth temperature: they grow between 52xc2x0 C. and 78xc2x0 C., no growth at 50xc2x0 C. or at 79xc2x0 C. The maximum growth rate was observed at about 70xc2x0 C. whereas the maximum cell yield was obtained at from about 63xc2x0 to about 64xc2x0 C.
Growth pH: pH in range: 7.2 to  greater than 10.5 supports growth. pH optimum: about 8.8 to about 9.5
Influence of NaCl: the optimum NaCl concentration for growth is 1% (w/v), with no growth above 4-5% (w/v).
Gram reaction: negative.
KOH reaction: negative.
Aminopeptidase reaction: negative.
Effect of SDS: in the presence of sodium dodecylsulphate 1%, (w/v) both the cells and the the sheath-like structures disappear under the microscope within a few seconds.
Effect of lysozyme: when lysozyme (10 mg/ml) was added to a suspension of cells under the microscope, little effect was observed. At 20 mg/ml lysozyme some of the rod-shaped cells became spherical.
Growth on
glucose: positive.
galactose: positive.
maltose: positive.
xylose: weak.
ribose: negative.
formate: negative.
acetate: positive.
lactate: negative.
propionate: negative.
pyruvate: weak.
glutamate: negative.
glycine: positive.
glycerol: positive.
ethanol: negative.
cellulose: positive.
casein: positive.
gelatine: positive.
xylan: positive.
starch: positive.
olive oil: positive.
tryptone: positive.
Influence of sulphur and hydrogen on growth: growth is inhibited by molecular hydrogen, H2. This inhibition may be relieved by the addition of sulphur to the medium.
G+C content: 36.3xc2x10.9 Mol % (n=2) (HPLC method).
Classification and Identification of the Microorganism
The strains of the invention were classified on the basis of phylogenetic relationships by direct sequencing of the 16S rRNA genes amplified by PCR. Sequences were compared with sequences for known bacteria accessed from GenBank and EMBL databases. Sequences were aligned and subjected to phylogenetic analysis using computer programs (versions 3.4 and 3.5c of the PHYLIP package (Felsenstein, J. (1989) Cladistics 5, 164-166)). Similarity values were computed (Table 3) and a phylogenetic tree constructed (FIG. 1).
The results indicate that the strains have a 16S rRNA sequence similarity of 98.7% and thus may be considered as isolates of the same species. The results further indicate that the strains of the new microorganism are more closely related to the genus Fervidobacterium than to bacteria of any other genus. However, the strains of the new microorganism have an outer sheath-like structure, often referred to as the xe2x80x98togaxe2x80x99 which is expanded over both poles of the rod-shaped cells. This xe2x80x98togaxe2x80x99 is a common feature of members of the genera Thermotoga, Thermosipho, Geotoga and Petrotoga Balows et al., Eds.) Springer-Verlag, New York, p. 3809-3815; Ravot, G. et al., (1995) International Journal of Systematic Bacteriology 45, 308-314). In contrast, Fervidobacterium species have a terminal xe2x80x98spheroidxe2x80x99 (Huber, R. and Stetter, K. O. ibid; Huber, R. et al., (1990) Archives of Microbiology 154, 105-111; Patel, B. K. C. et al., (1985) Archives of Microbiology 141, 63-69). This evidence alone indicates that the strains of the new microorganism represent a novel species. However, the difference in sequence homology of almost 10% with Fervidobacterium is highly significant since these lineages which represent one of the deepest branches of the Domain Bacteria (Winkler, S. and Woese, C. R. (1991) Systematic and Applied Microbiology 13, 161-165) are evolving slowly relative to other bacterial lineages (Huber, R. et al., Systematic and Applied Microbiology 12, 32-37). This indicates that the new bacterium is of a separate and hitherto unknown genus. On this basis the microorganism is assigned to the new genus, Thermopallium; and the strains of the microorganism to the species, Thermopallium natronophilum. The genus Thermopallium and the species Thermopallium natronophilum are defined by the nucleotide sequence of the 16S rRNA gene (SEQ ID No. 1 of the attached sequence listing), and by the phenotypic characteristics described herein.
The difference in G+C value compared with those of known species (Table 4) further supports the assignment of these new strains of the microorganism to a new species. The phenotypic characteristics of the microorganisms of the present invention clearly set them apart from the known species of the Thermotogales (Table 1). The novel microorganisms are clearly extreme thermophiles and have a temperature profile typical of Thermotogales species isolated from continental hot springs (i.e. non-marine sources). However, the known species of the Thermotogales all have pH optima for growth around neutrality. In contrast, the novel microorganisms of this invention are clearly obligately alkaliphilic and are unable to grow at neutral pH (Table 1) or without a medium containing carbonate anions.
1. Thermopallium natronophilum 36.3
2. Fervidobacterium islandicum 40
3. Fervidobacterium pennavorens 40.0
4. Fervidobacterium nodosum 33.7
5. Thermosipho africanus 30
6. Thermotoga maritima 46
7. Thermotoga thermarum 40
8. Geotoga petraea 29.5
9. Petrotoga miotherma 39.8
Cultivation of the Microorganism
The microorganism of the present invention can be cultivated only under strictly anoxic conditions, for example in a Freter type anaerobic cabinet or in closed bottles using the strictly anaerobic techniques described by Balch et al. (Microbiol. Rev. (1979), 43, 260-296). A suitable nutrient medium is required, Typically, such a medium comprises an assimilable carbon and nitrogen source together with other essential nutrients. Preferably, the total dissolved salt concentration of the medium does not exceed a conductivity value of about 15 mS/cm, and is prepared under the strictly anaerobic conditions indicated above. Preferably, a reductant is added to give a sufficiently low initial redox value. Suitable media can be prepared by techniques known in the art.
Since the natural isolates of the novel microorganisms of the novel species Thermopallium natronophilum of the present invention are alkaliphilic and are unable to grow below pH 7.2, the cultivation is preferably conducted at alkaline pH values which can be achieved by the addition of suitable buffers such as sodium carbonate, or more preferably mixtures of sodium carbonate and sodium bicarbonate, after sterilization of the growth medium, and preferably under a head space gas phase of O2-free N2. Such a medium is TMZ-medium which is a modification of Thermus medium using Castenholtz salts (Williams, R. A. D. and Da Costa, M. S. (1992) The genus Thermus and related microorganisms, in: The Prokaryotes (A. Barlows et al., eds.), Springer-Verlag, New York, p. 3745) adapted to the original conditions in the hot spring water from which the microorganism was isolated in pure culture. Growth is possible in other buffer mixtures such as Tris/HCl or Borax/NaOH provided that the pH is adjusted with carbonate. Little or no growth is obtained on media adjusted to alkaline pH values with NaOH.
For cultivation on a large scale it is typically necessary to sparge the medium continuously using O2-free nitrogen gas.
Minimum temperature for growth was about 40xc2x0 C. In a preferred embodiment, isolates of the novel species Thermopallium natronophilum were grown at 65xc2x0 C.
After fermentation, liquid enzyme concentrates may be obtained by separation of the cells from the culture broth and concentration of the broth using methods known in the art. Alternatively, the cells may be suspended in a suitable liquid and broken open, disintegrated, or dissolved, or otherwise treated to release enzymes in a soluble fraction, using appropriate methods. The solubilised enzymes may be purified, optionally after concentrating and/or precipitated in a solid form by the use of salts or water miscible solvents or removal of water. The purified enzymes may finally be obtained in a crystalline form.
Enzymes from the Microorganism
The enzymes of this invention are obtainable by the cultivation of a microorganism of the invention, preferably Thermopallium natronophilum Tg9A, DSM 9460, or a variant or mutant thereof, in an appropriate nutrient medium maintained at an alkaline pH, for example pH 7.5 to 12.0, or more preferably pH 8.5 to 9, by the addition of carbonate, or mixtures of carbonate and bicarbonate, containing carbon and nitrogen sources and inorganic salts.
A mutant or variant strain of Thermopallium natronophilum may be obtained spontaneously, chemically, by genetic manipulation techniques or otherwise and include mutants obtained by nucleic acid transfer, environmental selection pressure, UV radiation and by the use of mutagenic chemicals known to those skilled in the art.
The enzymes may also be obtained by recombinant DNA technology by cloning the appropriate genes in a suitable host organism. This may be achieved by any suitable means, and for example by digesting chromosomal DNA with one or more restriction enzymes to create a genomic library or random DNA fragments of one size. The DNA fragments from the library of the random fragments may be inserted into a recombinant nucleic acid. Such a recombinant nucleic acid is typically a vector, which may, for example, be a plasmid, a bacteriophage or any other construct which is suitable for the transfer, or for the transfer and expression, of nucleic acid sequences.
Those of skill in the art will be able to prepare suitable vectors starting with widely available vectors which will be modified by genetic engineering techniques known in the art, such as those described by Sambrook et al (Molecular cloning: a Laboratory Manual; 1989).
A vector of the invention typically comprises one or more origins of replication so that it can be replicated in a host cell, such as bacterial cell or yeast cell (this enables constructs to be replicated and manipulated, for example in E. coli, by standard techniques of molecular biology). A vector also typically comprises at least the following elements, usually in a 5xe2x80x2 to 3xe2x80x2 arrangement: a promoter for directing the expression of a nucleic acid sequence encoding an enzyme of the invention; optionally a regulator of the promoter, a transcription start site, a translational start codon; and a nucleic acid sequence encoding an enzyme of the invention.
The vector may also contain one or more selectable marker genes, for example one or more antibiotic resistance genes. Such marker genes allow identification of transformants. Optionally, the vector may also comprise an enhancer for the promoter. The vector may also comprise a polyadenylation signal, typically 3xe2x80x2 to the nucleic acid encoding the enzyme of the invention. The vector may also comprise a transcriptional terminator 3xe2x80x2 to the sequence encoding the enzyme of the invention.
The vector may also comprise one or more introns or other non-coding sequences, for example 3xe2x80x2 to the sequence encoding the polypeptide of interest.
In a typical vector, the nucleic acid sequence encoding the enzyme of the invention is operably linked to a promoter capable of expressing the sequence. xe2x80x9cOperably linkedxe2x80x9d refers to a juxtaposition wherein the promoter and the nucleic acid sequence encoding the enzyme of the invention are in a relationship permitting the coding sequence to be expressed under the control of the promoter. Thus, there may be elements such as 5xe2x80x2 non-coding sequence between the promoter and coding sequence. Such sequences can be included in the vector if they enhance or do not impair the correct control of the coding sequence by the promoter.
Any suitable promoter capable of directing expression of the nucleic acid encoding the therapeutic polypeptide or protein may be included in the vector. For example, the promoter may be a bacterial, eukaryotic or viral promoter. The promoter may be constitutive or inducible.
Thus, the invention provides host cells comprising one or more recombinant nucleic acids of the invention. These cells are typically transformed or transfected with the recombinant nucleic acid. The recombinant nucleic acid may be introduced into the host cell by any suitable means. For example, sequences encoding enzymes of the invention may be packaged into infectious viral particles in order to transfect cells. The nucleic acid sequences encoding enzymes of the invention may also be introduced by electroporation, lipofection, biolistic transformation or by simply contacting the nucleic acid sequences with cells in solution.
Such vectors may replicate either after integration into the host cell genome or remain extrachromosomal, as in the case of plasmids. Any suitable host cell may be used, including both prokaryotic and eukaryotic microbes, and plant cells.
Recombinant clones may be selected using generally available techniques, such as screening for the presence of a marker. One suitable screening methods include nucleic acid hybridisation, antibody assays and plate assays for the detection of protein activity.
If the enzyme of interest is secreted, it may be recovered from the growth medium by conventional techniques. Alternatively, it can be recovered from the host cells by disrupting them, and then using recovery techniques known in the art.
Thermopallium natronophilum, a specific novel microorganism of this invention, has been found to produce valuable novel enzymes, in particular, amylases, cellulases, lipases, proteases, pullulanases and xylanases. As an illustration, the properties of the amylases of the invention will be described.
Properties of the Amylases Produced by the Microorganism
The molecular weight of the soluble amylase fraction separated from the growth medium by gel-filtration chromatography is 90 kDa, by comparison with protein markers. This amylase fraction has an optimum temperature for amylase activity of 95xc2x0 C. and an optimum pH of 8.8 (FIG. 2 and FIG. 3).
Two amylases can be separated by ion exchange chromatography and give the following molecular weights when examined by SDS-polyacrylamide electrophoresis:
Amylase A-I subunit molecular weight=87 kDa
Amylase A-II subunit molecular weight=83 kDa.
Amylase A-I has an optimum temperature of 95xc2x0 C. and optimum pH of 10.2 (FIG. 4 and FIG. 5). The half-life of its activity is 11 minutes measured at 96xc2x0 C.
Amylase A-II has an optimum temperature of 80xc2x0 C. and an optimum pH of 9.6 (FIG. 6 and FIG. 7). No enzyme activity is lost during incubation at 80xc2x0 C. for 120 minutes.
The amylases have the following further characteristics.
Amylase A-I
Hydrolytic activity on soluble starch producing primarily maltose and other dextrins.
Hydrolytic activity on pullulanan.
Activity is enhanced by NaCl (0.0067M)
Amylase A-II
Hydrolytic activity on soluble starch producing dextrins (G1-G9).
Activity reduced by EDTA and EGTA.
Requires Ca2+ for activity.
Amylase A-I has the N-terminal amino acid sequence:
Xaa-Xaa-Glu-Ile-Ile-Tyr-Val/Asp-Gly-Phe
(where Xaa represents any amino acid); and contains the (internal) partial amino acid sequence:
Tyr-Ile-Gly-Asp-Gly-Ala-(Trp)-Glu-Ala-Val-Leu-Glu-Gly-(Asp)-(Asp)-Glu-(Gly/Glu)-Phe-Tyr-Arg
(where brackets indicate uncertainty about the identity of the amino acid).
Amylase A-II all comprises the (internal) partial amino acid sequence:
Ile-Gly-Leu-Pro-Ser-Val-Met-Thr-Glu-Pro-Trp-Asn-Pro-Ile-Gly-Gly-Ser-Asn-(Trp)-Ile-Phe-Asp-Met-Met-Leu-Ile-(Arg).
Amylases A-I and A-II are preferred amylases of the invention, but the invention is not limited to these amylases. Rather, the invention also provides variants of these amylases with slightly different amino acid sequences, and the nucleic acid sequences encoding these variants.
A variant amylase of the invention typically has a high degree of sequence homology to Amylase A-I or Amylase A-II, for example up to 70%, up to 80%, up to 90%, up to 95%, or up to 99% sequence homology.
A variant may have a sequence which differs from that of Amylase A-I or Amylase A-II by one or more deletions, substitutions or insertions, as long as the variant has the amylase activity of Amylase A-I or Amylase A-II, or substantially that activity. For example, variants typically have hydrolytic activity on some or all of the substrates on which Amylase A-I and/or A-II have hydrolytic activity.
Utility of the Invention
Enzymes obtained from the novel organisms may be used in the detergent industry in laundry detergents and automatic dishwashing detergents. Due to their thermostability and alkaline nature, these enzymes are extremely suitable to be used at high temperatures at high pH. In other words, they are extremely suitable to be used under conditions which are ideal for washing, especially for dishwashing. Examples of enzymes which may be used in both powder and liquid detergents for the degradation of stains and soil are amylases for the degradation of carbohydrates, proteases for the degradation of protein and lipases for the degradation of lipids. If the enzymes. are used in compositions, such as for example in detergent compositions, they may be used in combination with many other detergent ingredients known in the art as, for example, builders, bleaching agents, bleach activators, softeners, perfumes, other enzymes etc.
The detergent industry is not the only industry interested in thermostable alkaline enzymes. Many useful applications for these enzymes are also found in the paper and pulp industry and the textile industry. For instance, thermostable alkaline amylases may be used for laundry detergents and automatic dishwashing detergents; but also for the manufacture of paper, especially desizing, and desizing of textiles, especially in combination with an alkaline scouring process.
It is this versatility of thermostable alkaline enzymes that explains the growing demand for these enzymes.